The free version doesn't support SSH/SFTP, so there is no cipher support.
The Pro version supports SSL/TLS, and SSH, which are both secure protocols. They support slightly different ciphers.
The SSH ciphers are blowfish-cbc,aes128-cbc,aes192-cbc,aes256-cbc,3des-cbc,aes128-ctr,aes192-ctr,and aes256-ctr.
For completeness, the SSL/TLS cipher suites are:
RSA_RC4_128_MD5
RSA_RC4_128_SHA
RSA_RC4_40_MD5
RSA_RC2_40_MD5
RSA_DES_56_SHA
RSA_3DES_168_SHA
RSA_DES_40_SHA
RSA_AES_128_SHA
RSA_AES_256_SHA
RSA_AES_128_SHA256
RSA_AES_256_SHA256
